| Previous DNA and RNA sequencing projects have provided a vast amount of sequence information. However, there is great deal of interest in secondary and tertiary structures formed, which will help researchers understand the function and interactions of nucleic acids.;Many naturally occurring RNA structures contain single mismatches. However, the algorithms currently used to predict structure from sequence are based on a minimal set of data which requires several approximations and assumptions. To improve the prediction of secondary structure, thermodynamic parameters for duplex formation were collected for the most frequently occurring single mismatches, single mismatches with G-U nearest neighbors, and single mismatches placed in three duplex positions. This data significantly increases the number of single mismatches with experimental values, which no longer need predictive values. Using linear regression least squares methods and experimental single mismatch thermodynamic data, single mismatch specific algorithms have been derived. These algorithms, along with the reported thermodynamics for frequently occurring single mismatches, should allow for improved calculation of the free energy of RNA duplexes containing this motif and, furthermore, allow for improved prediction of secondary structure from sequence.;To improve the prediction of RNA tertiary structure, RNA structures containing single mismatches available in the Protein Data Bank were systematically located, annotated, and compared to identify structural patterns. Together, the thermodynamic and structural data will be used to help improve the accuracy of secondary and tertiary structure prediction from sequence for RNAs containing single mismatches. To further improve the prediction of RNA tertiary structure, a database compiling a multitude of DNA and RNA secondary structure motifs has been created and is currently being implemented into a web-based, user-friendly search program.;To investigate the role of RNA thermodynamics and structure in RNA-protein interactions, the complement C5 protein and aptamer is used as a model system. This study utilized three different experimental procedures, optical melting and NMR experiments of the C5 aptamer, aptamer mimics, and aptamer mutants individually and in the presence of the C5 protein and fluorescence polarization experiments to probe the interaction between the RNA and the C5 protein. |
